Changeset 1947

Timestamp:

May 6, 2009, 4:23:51 PM (12 years ago)

Author:

Jari Häkkinen

Message:

Addresses #535. NaNs? are replaced with Inf in sorting in qQuantileNormalizer.

Location:

branches/0.5-stable

Files:

• test/Makefile.am (modified) (2 diffs)
• yat/normalizer/qQuantileNormalizer.h (modified) (4 diffs)

branches/0.5-stable/test/Makefile.am

@@ -7 +7 @@
 # Copyright (C) 2005 Jari Häkkinen, Peter Johansson
 # Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson, Markus Ringnér
-# Copyright (C) 2009 Peter Johansson
+# Copyright (C) 2009 Jari Häkkinen, Peter Johansson
 #
 # This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -65 +65 @@
 
 # tests not passing through yet
-XFAIL_TESTS = normalization_test
+XFAIL_TESTS =
 
 TESTS += documentation_test.sh

branches/0.5-stable/yat/normalizer/qQuantileNormalizer.h

@@ -261 +261 @@
 
     std::vector<size_t> sorted_index(last-first);
-    utility::sort_index(first, last, sorted_index);
+    // Code to avoid problems with NaN (ticket:535)
+    // utility::sort_index(first, last, sorted_index);
+    // ... above statement replaced below code block
+    {
+      utility::Vector vec(std::distance(first, last));
+      std::copy(first, last, vec.begin());
+      for (utility::Vector::iterator i(vec.begin()); i!=vec.end(); ++i)
+        if (std::isnan((*i)))
+          *i = std::numeric_limits<double>::infinity();
+      utility::sort_index(vec.begin(), vec.end(), sorted_index);
+    }
+    // end Code to avoid problems with NaN (ticket:535)
 
     utility::Vector diff(source.averages());
@@ -322 +333 @@
 
     std::vector<size_t> sorted_index(last-first);
-    utility::sort_index(utility::data_iterator(first), 
-                        utility::data_iterator(last), sorted_index);
+    // Code to avoid problems with NaN (ticket:535)
+    // utility::sort_index(utility::data_iterator(first),
+    //                     utility::data_iterator(last), sorted_index);
+    // ... above statement replaced below code block
+    {
+      using namespace utility;
+      std::vector<DataWeight> vec;
+      vec.reserve(std::distance(first, last));
+      std::back_insert_iterator<std::vector<DataWeight> > inserter(vec);
+      std::copy(first, last, inserter);
+      for (std::vector<DataWeight>::iterator i(vec.begin()); i!=vec.end(); ++i)
+        if (std::isnan((i->data())))
+          i->data() = std::numeric_limits<double>::infinity();
+      utility::sort_index(utility::data_iterator(vec.begin()),
+                          utility::data_iterator(vec.end()), sorted_index);
+    }
+    // end Code to avoid problems with NaN (ticket:535)
 
     utility::Vector diff(source.averages());
@@ -377 +403 @@
     utility::Vector vec(std::distance(first, last));
     std::copy(first, last, vec.begin());
+    // Code to avoid problems with NaN (ticket:535)
+    for (utility::Vector::iterator i(vec.begin()); i!=vec.end(); ++i)
+      if (std::isnan((*i)))
+        *i = std::numeric_limits<double>::infinity();
+    // end Code to avoid problems with NaN (ticket:535)
     std::sort(vec.begin(), vec.end());
     init(vec, N);
@@ -388 +419 @@
                                                utility::weighted_iterator_tag)
   {
-    std::vector<utility::DataWeight> vec;
+    using namespace utility;
+    std::vector<DataWeight> vec;
     vec.reserve(std::distance(first, last));
-    std::back_insert_iterator<std::vector<utility::DataWeight> > inserter(vec);
+    std::back_insert_iterator<std::vector<DataWeight> > inserter(vec);
     std::copy(first, last, inserter);
+    // Code to avoid problems with NaN (ticket:535)
+    for (std::vector<DataWeight>::iterator i(vec.begin()); i!=vec.end(); ++i)
+      if (std::isnan((i->data())))
+        i->data() = std::numeric_limits<double>::infinity();
+    // end Code to avoid problems with NaN (ticket:535)
     std::sort(vec.begin(), vec.end());
     init(vec, N);